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Plants must adapt to drought and high-salinity stresses in order to survive. Molecular and genomic studies have shown that many genes with various functions are induced by drought and high-salinity stresses, and that the various signaling factors are involved in the stress responses. The development of microarray-based expression profiling methods, together with the availability of genomic and/or cDNA sequence data, and gene-knock-out mutants, has allowed significant progress in the characterization of the plant stress response. Recent studies also revealed that small RNAs, RNA processing and chromatin regulation are involved in the abiotic stress responses. In this review, we highlight recent progress in the research on the transcriptome for the response to plant drought and salt stress

Metabolomics aims for comprehensive analysis of the metabolic complement. The metabolic phenotype is typically described by changes in metabolic pool sizes. Today investigations are technologically limited to a few hundred metabolites. Metabolomics studies are typically restricted to a single analytical technology, such as GC-TOF-MS which will be the focus technology of this chapter. Two strategies for data analysis are applied. Metabolite fingerprinting investigates all analytical signals. Metabolite profiling considers only information which represents known metabolites. In the last 8–10 years functional metabolome analysis has passed from concept discussion, method development and feasibility assessment into a phase of method automation and increased scope of applications for enhanced hypothesis generation. It is, however, still an early time for lessons to be learned from high-throughput metabolome analyses. This chapter attempts to exemplify the potential of metabolome analysis for the screening of genetic diversity selected by breeding. This diversity is a widely recognized but also a hard to investigate biological resource. In land races, selection has lead to successful adaptation, for example towards environmental stress tolerance. However, the underlying genomic changes remain elusive. Metabolic phenotyping analysis may circumvent the problem by identifying metabolic markers for a targeted selection. Ultimately metabolic profiling may allow an initial functional insight into metabolic modes of tolerance acquisition without prior knowledge of genomic modifications

Plant responses to water and salinity stress have been studied extensively. Perception of and adaptation to salt and drought stress take place with time scales that vary from seconds to months. Several important signaling intermediates have been identified that contribute to this process including the second messengers Ca, IP and cGMP, hormones such as ABA, regulatory proteins such as kinases and phosphatases, and many specific transcription factors. Extensive available data allow us to build up a simplified chronological record which indicates that initial osmosensing may rely on the action of specific receptor kinases and/or mechanosensitive ion channels. Second messengers are responsible for the subsequent signal transduction to the nucleus where transcription factors, for example of the DREB family, induce gene transcription. The upregulation of hormone synthesis, particularly of ABA, instigates a cascade of responses including altered transcription of many genes. Ultimately, these signaling events lead to changed activity of target proteins such as those involved in compatible osmolyte synthesis and the transport of water and ions

In the last decade, the sequencing of several plant genomes has greatly amplified the number of genes being evaluated for their ability to confer stress tolerance. Over 50 genes have been reported to confer drought tolerance when overexpressed and the number of field trials for transgenic drought tolerant crops is on the rise. Nevertheless, no transgenic drought tolerant crop has yet been commercialized. In this chapter, we examine the approaches being taken by academic labs and the agricultural biotechnology industry to identify and evaluate candidate genes. We address criteria used for selecting candidate genes, developing high-throughput phenotyping platforms and applying drought stress in the lab. In addition, we highlight promising genes that are at more advanced stages of evaluation

Salt tolerance in plants is a complex trait, which involves multiple genes participating in a myriad of processes that limit uptake, promote efflux, enhance vacuolar storage of Na and recycle Na from shoots to roots. In addition, the suppression of high Na-triggered oxidative stress and cell death also increases salt tolerance. A number of salt tolerance genes have been identified and characterized using arabidopsis and rice as model plants. Mutant screens have been frequently utilized and most genes identified with this approach are overly-sensitive to salt stress, genes, implying that positive gene function is required for salt tolerance. To identify genes that positively contribute to salt tolerance and are more easily transferred to crops, Ceres has developed a large population of arabidopsis transgenic lines overexpressing genes from several species and used a seed pooling strategy to screen these for enhanced salt tolerance. Thus far, we have identified 10 genes that when overexpressed result in increased salt tolerance. The encoded proteins are related to calmodulin, calmodulin-binding, zinc-finger, putative cyclases, stress-related and novel proteins. These genes may be involved in the regulation of and/or genes, as well as the suppression of high Na-triggered generation of reactive oxygen species and cell death. We discuss methods, such as stacking genes that provide different mechanisms for salt tolerance or using salt inducible promoters, to develop super-tolerant cultivars of crops to be grown in high salinity soils

Compared to conventional breeding approaches, the dissection of the genetic basis of quantitative traits into their single components (i.e. Quantitative Trait Loci: QTLs) provides a more direct access to valuable allelic diversity at the loci governing the adaptive response to drought and salinity. Genomics and post-genomics platforms offer unprecedented opportunities to map, clone and manipulate the suite of QTLs affecting tolerance to drought and salinity in model species and crops. New high-throughput platforms capable of reducing the cost of molecular profiling coupled with a rapidly expanding amount of sequence information will streamline QTL dissection and the identification of superior alleles to enhance tolerance to drought and/or salinity. Therefore, it is expected that yield improvement under drought and/or saline conditions will increasingly benefit from the manipulation of QTLs through marker-assisted selection and, following QTL cloning, genetic engineering. Approaches based on the screening of wild relatives will unveil new allelic variants lost during domestication and early selection. Allele mining (e.g. association mapping, TILLING) in germplasm and mutant collections coupled with marker-assisted backcrossing and/or genetic engineering will further expand the possibilities to improve elite materials. QTL-based modelling approaches will contribute to better understand ‘Genotype x Environment’ interactions and to single out the most promising genotypes based upon the available QTL information. The impact of QTL-based approaches on the release of improved cultivars more resilient to drought and salinity will depend on their successful integration with conventional breeding methodologies and a thorough understanding of the biochemical and physiological processes limiting yield under such adverse conditions.

Salt accumulation in soil surfaces, known as soil salinity, could lead to the impairment of plant growth and development and is manifested mostly under irrigated and dryland agriculture. Excess salts in the soil affects plants through osmotic stress; accumulation to toxic levels within the cells; and through the interference with the uptake of mineral nutrients. Rice productivity in several parts of the world is therefore severely limited by salinity on account of the prevalence of irrigation in rice farming. Tolerance to salt toxicity in plants is a genetic and physiologically complex trait. Halophytes (salt tolerant plants) are different from the salt-sensitive glycophytes in terms of peculiarities in their anatomy, ability to sequester otherwise toxic ions, and other physiologic processes. It is logical therefore to infer complexity also at the genetic level on account of the several pathways involved in these mechanisms. These complexities have confounded genetic improvement strategies for salinity tolerance in plants resulting in a paucity of saline tolerant plants, with only about 30 officially released saline tolerant crop varieties world-wide. Only one saline tolerant rice variety, Bicol, has been officially released to farmers. We review strategies being currently employed in the development of saline tolerant rice varieties. These include conventional plant breeding which is hampered by the lack of suitable genetic variation for this trait; the modest progress made through doubled haploidy; and the reliance on somaclonal variation, an unsustainably unpredictable strategy. This review also posits that while genetic transformation has led to the modification of certain physiological indices implicated in salinity tolerance in rice, in isolation, these modifications have not been translated to improved yield under salt stress. A more recently adopted strategy, induced mutagenesis, has led to some promising results. We argue that the production of induced rice mutants holds the greatest promise of these strategies for mitigating the scourge of soil salinity considering the relative ease with which other traits in this crop have been modified using this methodology. The underlying principles of induced mutagenesis; the modes of action of different mutagenic agents; and procedures for the rapid production and detection of mutants are also summarised. In order to enhance efficiency in the production, detection and incorporation of induced mutants into crop improvement programmes, we suggest the coupling of (such as doubled haploidy and cell suspension cultures) and molecular genetic techniques to this methodology. It is posited also that the efficiency of this process can be greatly enhanced by marker-aided selection while high throughput reverse genetics strategies could lead to the rapid detection of mutation events in target genes. It is concluded that with the plethora of genomics resources available for rice, the use of induced mutations for improving salinity tolerance (and other traits) would rely significantly on the concerted application of efficiency enhancing techniques and functional genomics strategies (including reverse genetics)

Although enormous effort has been put into conventional breeding programmes for both drought and salt tolerance, there has been little progress in producing varieties that are adopted by farmers in their fields. This is largely due to the lack of consideration given to the specific needs of farmers in droughted and salt-affected environments, in particular in terms of non-yield post-harvest traits. We discuss with examples the advantages and disadvantages of participatory variety selection (PVS) and participatory plant breeding (PPB) in their various forms, as well as the use of the term client-oriented breeding to describe the process of involving the end-users of the breeding programme. Methods for the analysis of participatory trials, and practical considerations for their management, are presented. We also show how both participatory and molecular approaches can be combined into an integrated, client-oriented breeding programme

The challenge that commercial breeders have in improving the yield of crops in drought-prone environments is to produce cultivars that capture more of the water supply for use in transpiration; exchange transpired water for CO more effectively in producing biomass; and convert more of the biomass into grain. Many traits affect these requirements, and assume greater or lesser importance depending on the severity and timing of a drought. Although hundreds of QTLs have been found that are associated with improved yield during drought, few have been converted into markers useful to breeders owing to the difficulty of understanding the phenotype in realistic environments. The few markers that are in use target disease resistance and morphological or ecophysiological traits known to affect the water economy of a crop. Faster progress in developing markers useful to breeders will come with the evidently increasing interaction between breeding programs and marker laboratories

In the past decade, the scientific community has witnessed a major leap in our understanding about how plant perceives and respond to abiotic stresses. Various candidates participating in this coordinated and orchestrated relays have been identified and their molecular mechanisms of operation have also been worked out. This analysis has clearly established a complex network of cellular machinery operative in plants under such conditions. Tools of functional genomics have been utilized to decipher the contributions of several of these individual components towards the complex stress response. Some of these studies have also been extended beyond model plants, and crop systems such as rice have been utilized to document the usefulness of some of these strategies towards genetic modifications of crop plants which are better adapted towards unfavorable environmental conditions. It is heartening to see the extension of few efforts beyond laboratory to field level testing. Indeed, a few of selected candidate genes have also passed these field level tests. However, it is also true that drought/salinity tolerant transgenic crop plants are yet away from the reach of farmers. A conscious deliberate and strategic action plan along with the right choice of battery of genes is required to achieve this important goal